Transcription initiation sites of prototype and variant JC virus early and late messenger RNAs

The locations of the authentic viral transcription initiation sites utilized during the course of a JCV(Mad1) infection of primary human fetal glial (PHFG) cells have been identified using the S1 nuclease and primer extension techniques. Early viral mRNA start sites were located 20 to 30 nucleotides (positions 89-92 and 5115-5125) downstream from the two TATA elements present within the promoter-enhancer region of the JCV(Mad1) strain. Absence of the distal TATA element, as seen in the JCV(Mad4) promoter-enhancer, resulted in the alteration of the position and intensity of these sites. Several start sites were observed for late viral mRNAs; two sites were located 25 and 35 nucleotides (positions 191-192 and 200-203) downstream from a potential surrogate TATA signal. To determine whether the presence of constitutively expressed JCV large T protein would alter the pattern of transcription initiation, RNA isolated from JCV(Mad1)-infected POJ cells was analyzed. Although the positions of the early and late viral mRNA start sites were similar to those observed in JCV(Mad1)-infected PHFG cells, they were detected earlier in the course of the infection.